med-cloud

dep: [med-config] (= 3.9.0)

Debian Med general config package

dep: [med-tasks] (= 3.9.0)

Debian Med tasks for tasksel

rec: [abyss]

de novo, parallel, sequence assembler for short reads

rec: [aevol]

digital genetics model to run Evolution Experiments in silico

rec: [alien-hunter]

Interpolated Variable Order Motifs to identify horizontally acquired DNA

rec: [altree]

program to perform phylogeny-based association and localization analysis

rec: [amap-align]

Protein multiple alignment by sequence annealing

rec: [ampliconnoise]

removal of noise from 454 sequenced PCR amplicons

rec: [aragorn]

tRNA and tmRNA detection in nucleotide sequences

rec: [arden]

specificity control for read alignments using an artificial reference

rec: [autodock]

analysis of ligand binding to protein structure

rec: [autodock-vina]

docking of small molecules to proteins

rec: [autogrid]

pre-calculate binding of ligands to their receptor

rec: [bamtools]

toolkit for manipulating BAM (genome alignment) files

rec: [bedtools]

suite of utilities for comparing genomic features

rec: [bioperl]

Perl tools for computational molecular biology

rec: [bioperl-run]

BioPerl wrappers: scripts

rec: [biosquid]

utilities for biological sequence analysis

rec: [bowtie]

Ultrafast memory-efficient short read aligner

rec: [bowtie2]

ultrafast memory-efficient short read aligner

rec: [boxshade]

Pretty-printing of multiple sequence alignments

rec: [bwa]

Burrows-Wheeler Aligner

rec: [cassiopee]

index and search tool in genomic sequences

rec: [cd-hit]

suite of programs designed to quickly group sequences

rec: [cdbfasta]

Constant DataBase indexing and retrieval tools for multi-FASTA files

rec: [circos]

plotter for visualizing data

rec: [clearcut]

extremely efficient phylogenetic tree reconstruction

rec: [clonalframe]

inference of bacterial microevolution using multilocus sequence data

rec: [clustalo]

General-purpose multiple sequence alignment program for proteins

rec: [clustalw]

global multiple nucleotide or peptide sequence alignment

rec: [concavity]

predictor of protein ligand binding sites from structure and conservation

rec: [conservation-code]

protein sequence conservation scoring tool

rec: [datamash]

statistics tool for command-line interface

rec: [dialign]

Segment-based multiple sequence alignment

rec: [dialign-tx]

Segment-based multiple sequence alignment

rec: [discosnp]

discovering Single Nucleotide Polymorphism from raw set(s) of reads

rec: [disulfinder]

cysteines disulfide bonding state and connectivity predictor

rec: [dnaclust]

tool for clustering millions of short DNA sequences

rec: [dssp]

protein secondary structure assignment based on 3D structure

rec: [embassy-domainatrix]

Extra EMBOSS commands to handle domain classification file

rec: [embassy-domalign]

Extra EMBOSS commands for protein domain alignment

rec: [embassy-domsearch]

Extra EMBOSS commands to search for protein domains

rec: [emboss]

European molecular biology open software suite

rec: [exonerate]

generic tool for pairwise sequence comparison

rec: [fastdnaml]

Tool for construction of phylogenetic trees of DNA sequences

rec: [fastlink]

faster version of pedigree programs of Linkage

rec: [fastqc]

quality control for high throughput sequence data

rec: [fasttree]

phylogenetic trees from alignments of nucleotide or protein sequences

rec: [fitgcp]

fitting genome coverage distributions with mixture models

rec: [flexbar]

flexible barcode and adapter removal for sequencing platforms

rec: [freecontact]

fast protein contact predictor

rec: [gasic]

genome abundance similarity correction

rec: [genometools]

versatile genome analysis toolkit

rec: [gff2aplot]

pair-wise alignment-plots for genomic sequences in PostScript

rec: [gff2ps]

produces PostScript graphical output from GFF-files

rec: [glam2]

gapped protein motifs from unaligned sequences

rec: [gmap]

spliced and SNP-tolerant alignment for mRNA and short reads

rec: [grinder]

Versatile omics shotgun and amplicon sequencing read simulator

rec: [gromacs]

Molecular dynamics simulator, with building and analysis tools

rec: [hhsuite]

sensitive protein sequence searching based on HMM-HMM alignment

rec: [hisat2]

graph-based alignment of short nucleotide reads to many genomes

rec: [hmmer]

profile hidden Markov models for protein sequence analysis

rec: [idba]

iterative De Bruijn Graph short read assemblers

rec: [infernal]

inference of RNA secondary structural alignments

rec: [jellyfish]

count k-mers in DNA sequences

rec: [kalign]

Global and progressive multiple sequence alignment

rec: [kissplice]

Detection of various kinds of polymorphisms in RNA-seq data

rec: [last-align]

genome-scale comparison of biological sequences

rec: [loki]

MCMC linkage analysis on general pedigrees

rec: [macs]

Model-based Analysis of ChIP-Seq on short reads sequencers

rec: [mafft]

Multiple alignment program for amino acid or nucleotide sequences

rec: [mapsembler2]

bioinformatics targeted assembly software

rec: [maq]

maps short fixed-length polymorphic DNA sequence reads to reference sequences

rec: [melting]

compute the melting temperature of nucleic acid duplex

rec: [minia]

short-read biological sequence assembler

rec: [mipe]

Tools to store PCR-derived data

rec: [mira-assembler]

Whole Genome Shotgun and EST Sequence Assembler

rec: [mlv-smile]

Find statistically significant patterns in sequences

rec: [mothur]

sequence analysis suite for research on microbiota

rec: [mrbayes]

Bayesian Inference of Phylogeny

rec: [mummer]

Efficient sequence alignment of full genomes

rec: [muscle]

Multiple alignment program of protein sequences

rec: [muscle3]

multiple alignment program of protein sequences

rec: [mustang]

multiple structural alignment of proteins

rec: [ncbi-epcr]

Tool to test a DNA sequence for the presence of sequence tagged sites

rec: [ncbi-tools-bin]

NCBI libraries for biology applications (text-based utilities)

rec: [ncoils]

coiled coil secondary structure prediction

rec: [neobio]

computes alignments of amino acid and nucleotide sequences

rec: [paraclu]

Parametric clustering of genomic and transcriptomic features

rec: [parsinsert]

Parsimonious Insertion of unclassified sequences into phylogenetic trees

rec: [pdb2pqr]

Preparation of protein structures for electrostatics calculations

rec: [perm]

efficient mapping of short reads with periodic spaced seeds

rec: [phyml]

Phylogenetic estimation using Maximum Likelihood

rec: [phyutility]

simple analyses or modifications on both phylogenetic trees and data matrices

rec: [picard-tools]

Command line tools to manipulate SAM and BAM files

rec: [plink]

whole-genome association analysis toolset

rec: [plink1.9]

whole-genome association analysis toolset

rec: [plink2]

whole-genome association analysis toolset

rec: [poa]

Partial Order Alignment for multiple sequence alignment

rec: [prank]

Probabilistic Alignment Kit for DNA, codon and amino-acid sequences

rec: [prime-phylo]

bayesian estimation of gene trees taking the species tree into account

rec: [primer3]

tool to design flanking oligo nucleotides for DNA amplification

rec: [probabel]

Toolset for Genome-Wide Association Analysis

rec: [probcons]

PROBabilistic CONSistency-based multiple sequence alignment

rec: [proda]

multiple alignment of protein sequences

rec: [prodigal]

Microbial (bacterial and archaeal) gene finding program

rec: [python3-biomaj3-cli]

BioMAJ client

rec: [python3-biopython]

Python3 library for bioinformatics

rec: [r-bioc-edger]

Empirical analysis of digital gene expression data in R

rec: [r-bioc-hilbertvis]

GNU R package to visualise long vector data

rec: [r-cran-pvclust]

Hierarchical Clustering with P-Values via Multiscale Bootstrap

rec: [r-cran-qtl]

GNU R package for genetic marker linkage analysis

rec: [r-cran-vegan]

Community Ecology Package for R

rec: [r-other-mott-happy.hbrem]

GNU R package for fine-mapping complex diseases

rec: [raster3d]

tools for generating images of proteins or other molecules

rec: [readseq]

Conversion between sequence formats

rec: [rnahybrid]

Fast and effective prediction of microRNA/target duplexes

rec: [rtax]

Classification of sequence reads of 16S ribosomal RNA gene

rec: [samtools]

processing sequence alignments in SAM, BAM and CRAM formats

rec: [seqan-apps]

C++ library for the analysis of biological sequences

rec: [sibsim4]

align expressed RNA sequences on a DNA template

rec: [sigma-align]

Simple greedy multiple alignment of non-coding DNA sequences

rec: [sim4]

tool for aligning cDNA and genomic DNA

rec: [smalt]

Sequence Mapping and Alignment Tool

rec: [snap]

location of genes from DNA sequence with hidden markov model

rec: [soapdenovo]

short-read assembly method to build de novo draft assembly

rec: [soapdenovo2]

short-read assembly method to build de novo draft assembly

rec: [sra-toolkit]

utilities for the NCBI Sequence Read Archive

rec: [ssake]

genomics application for assembling millions of very short DNA sequences

rec: [staden-io-lib-utils]

programs for manipulating DNA sequencing files

rec: [t-coffee]

Multiple Sequence Alignment

rec: [tabix]

generic indexer for TAB-delimited genome position files

rec: [theseus]

superimpose macromolecules using maximum likelihood

rec: [tigr-glimmer]

Gene detection in archea and bacteria

rec: [tree-puzzle]

Reconstruction of phylogenetic trees by maximum likelihood

rec: [tree-ppuzzle]

Parallelized reconstruction of phylogenetic trees by maximum likelihood

rec: [vcftools]

Collection of tools to work with VCF files

rec: [velvet]

Nucleic acid sequence assembler for very short reads

rec: [veryfasttree]

Speeding up the estimation of phylogenetic trees from sequences

rec: [wise]

comparison of biopolymers, like DNA and protein sequences

sug: acedb-other

Package not available

sug: anfo

Package not available

sug: bagpipe

Package not available

sug: blast2

Package not available

sug: [cufflinks]

Transcript assembly, differential expression and regulation for RNA-Seq

sug: embassy-phylip

Package not available

sug: giira

Package not available

sug: python3-cogent3

Package not available

sug: qiime

Package not available